hierarchy_tools.h File Reference

A set of useful functionality on IMP::atom::Hierarchy decorators. More...

#include <IMP/atom/atom_config.h>
#include <IMP/algebra/algebra_config.h>
#include "Hierarchy.h"
#include "Residue.h"
#include "Atom.h"
#include <IMP/core/Typed.h>
#include <IMP/core/XYZR.h>
#include "Selection.h"
#include <boost/graph/adjacency_list.hpp>
#include <boost/unordered_map.hpp>

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Classes
class	IMP::atom::HierarchiesGeometry
	Display an IMP::SingletonContainer of IMP::atom::Hierarchy particles as balls. More...
class	IMP::atom::HierarchyGeometry
	Display an IMP::atom::Hierarchy particle as balls. More...

Namespaces
	IMP
	Base functionality and abstract base classes for representation, scoring and sampling.
	IMP::atom
	Functionality for loading, creating, manipulating and scoring atomic structures.

Typedefs
typedef boost::graph	IMP::atom::HierarchyTree
	A graph for representing a Hierarchy so you can view it nicely. More...
typedef HierarchyTree::EdgeNameMap	IMP::atom::HierarchyTreeConstEdgeName
typedef HierarchyTree::VertexNameMap	IMP::atom::HierarchyTreeConstVertexName
typedef HierarchyTree::edge_descriptor	IMP::atom::HierarchyTreeEdge
typedef boost::graph_traits < HierarchyTree >	IMP::atom::HierarchyTreeTraits
typedef HierarchyTree::vertex_descriptor	IMP::atom::HierarchyTreeVertex

Functions
Restraint *	IMP::atom::create_excluded_volume_restraint (const Hierarchies &hs, double resolution=-1)
Hierarchy	IMP::atom::create_protein (Model *m, std::string name, double target_radius, int number_of_residues, int first_residue_index=0, double volume=-1)
	Create a coarse grained molecule. More...
Hierarchy	IMP::atom::create_protein (Model *m, std::string name, double target_radius, const Ints domain_boundaries)
Hierarchy	IMP::atom::create_simplified_assembly_from_volume (Hierarchy h, double resolution)
Hierarchy	IMP::atom::create_simplified_from_volume (Hierarchy h, double resolution)
HierarchyTree	IMP::atom::get_hierarchy_tree (Hierarchy h)
	Get a graph for the passed Hierarchy. More...
HierarchyTreeVertexIndex	IMP::atom::get_vertex_index (const HierarchyTree &g)
void	IMP::atom::setup_as_approximation (Particle *h, const ParticlesTemp &other)
void	IMP::atom::setup_as_approximation (Hierarchy h)
void	IMP::atom::show_as_graphviz (const HierarchyTree &name, TextOutput out)
void	IMP::atom::transform (Hierarchy h, const algebra::Transformation3D &tr)
	Transform a hierarchy. This is aware of rigid bodies. More...

Simplification along backbone
These two methods create a simplified version of a molecule by merging residues sequentially. In one case every n residues are merged, in the other, the intervals are passed manually. The resulting molecule is not optimized by default and has no restraints automatically created. At the moment, the calls only support unmodified hierarchies loaded by read_pdb() which have only protein or DNA members. They return Hierarchy() if the input chain is empty. If keep_detailed is true, then the original high resolution structure particles are added as children of the simplified structure.
Hierarchy	IMP::atom::create_simplified_along_backbone (Hierarchy input, int num_res, bool keep_detailed=false)
Hierarchy	IMP::atom::create_simplified_along_backbone (Chain input, const IntRanges &residue_segments, bool keep_detailed=false)

Finding information
Get the attribute of the given particle or throw a ValueException if it is not applicable. The particle with the given information must be above the passed node.
Ints	IMP::atom::get_residue_indexes (Hierarchy h)
ResidueType	IMP::atom::get_residue_type (Hierarchy h)
AtomType	IMP::atom::get_atom_type (Hierarchy h)
std::string	IMP::atom::get_domain_name (Hierarchy h)

Detailed Description

A set of useful functionality on IMP::atom::Hierarchy decorators.

Copyright 2007-2021 IMP Inventors. All rights reserved.

Definition in file hierarchy_tools.h.